Search form

You are here

Support for science

Funded by EXDCI-2, EPCC is organising a 2-day workshop in Edinburgh on 8-9 July 2019 to present ideas on how science and engineering can be supported from Raspberry Pis to large scale supercomputers. We are looking to investigate how to introduce these topics to school-age audiences including linking to existing school curricula. This will include examples of existing education materials and activities and looking ahead to current plans.

The Software Sustainability Institute's (SSI) Collaborations Workshop 2019 (CW19) will be held at the West Park Teaching Hub, Loughborough University, Loughborough from 1-3 April 2019. This year the workshop will be themed around topics based on interoperability, documentation, training, and sustainability. Keynote speakers will include Catherine Stihler, CEO of Open Knowledge International, and Franziska Heine (link points to a German article), Head of Software & Development at Wikimedia Deutschland. They will open the event on 1st April.

Analysing genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation.

Typically in a cancer genomics analysis, both a tumour sample and a “normal” sample from the same individual are first sequenced using NGS systems and compared using a series of quality control stages. The first control stage, ‘Sequence Quality Control’ (which is optional), checks sequence quality and performs some trimming. While the second one, ‘Alignment’, involves a number of steps, such as alignment, indexing, and recalibration, to ensure that the alignment files produced are of the highest quality as well as several more to guarantee the variants are called correctly. Both stages compromise a series of intermediately computing and data-intensive steps that very often are handcrafted by researchers and/or analysts.

Earlier this year, HPE announced the Catalyst UK programme: a collaboration with Arm, SUSE and three UK universities to deploy one of the largest Arm-based high performance computing (HPC) installations in the world. EPCC was chosen as the site for one of these systems; the other two are the Universities of Bristol and Leicester.

EPCC's system (called 'Fulhame' after pioneering chemist Elizabeth Fulhame) was delivered and installed in early December. This HPE Apollo 70-based system consists of 64 compute nodes with two 32-core Cavium ThunderX2 processors (ie 4096 cores in total), 128GB of memory composed of 16 DDR4 DIMMs, and Mellanox InfiniBand interconnects. It will be made available to both industry and academia, with the aim to build applications that drive economic growth and productivity as outlined in the UK government’s Industrial Strategy.

PickCells is image analysis software developed by the Centre for Regenerative Medicine (CRM) at The University of Edinburgh. PickCells allows biologists to explore multidimensional biological images of stem cell niches, organoids, and embryos. In late October, with the assistance of six researchers, we evaluated the usability of PickCells to help guide its future development.

The meeting was attended by around 50 participants, an interesting mix of researchers, software developers, systems admins and research support/management staff, from the University of Edinburgh and Heriot-Watt University. It is intended to keep these gatherings open to all Higher Education and research institutions of the Edinburgh area.

The embedded Computational Science and Engineering (eCSE) programme has allocated funding to the UK computational science community over a period of six years. Integral to ARCHER, the National HPC Service, there has been a series of regular eCSE Calls to fund software development activities.

The last of the Calls has now closed and all funding has been allocated. Although a number of projects are still on-going, this seems a good time to review the benefits of the programme and to see whether its aims have been met.